Creating hexagonal grid which is a manifold
You could create the hexagonal grid using the 

add mesh extra objects Add-on

(Access the system preferences with Ctrl Alt U):



Then press ShiftA Add->Mesh->Extras->Honeycomb



And set the controls in the toolshelf to the size, nuber of columns and rows that you need for your project.





Use a solidify modifier to give it height and then use a bevel modifier to round the edges a bit.



The mesh will work fine with a boolean modifier: